MicroSatellite

Microsatellites, also known as short tandem repeats (STRs) or simple sequence repeats (SSRs), are repeating units of 1-6 base pairs scattered throughout genomes. Common motif lengths include dinucleotide repeats (for example CA), as well as tri- and tetranucleotide repeats. The number of repeat units at a given locus is highly variable among individuals, making microsatellites highly polymorphic. They are widespread in both coding and noncoding regions, with higher density in noncoding regions.

Genetic variation at microsatellite loci arises mainly by slipped-strand mispairing during DNA replication and by less frequent events such as recombination or indels; mutation rates are high relative to other genomic regions and depend on motif length, number of repeats, and flanking sequence context. One consequence is high heterozygosity, which makes these loci useful for distinguishing individuals in genetic analyses.

Laboratory analysis relies on PCR amplification of short flanking sequences surrounding the repeat to produce amplicons whose length reflects the number of repeats. Capillary electrophoresis or other sizing technologies resolve alleles by fragment length; results are often reported as repeat-number alleles. Common limitations include stutter peaks, allele dropout, or null alleles due to mutations in primer binding sites.

Applications span genetics and forensics: genetic linkage mapping, population and conservation genetics, parentage and identity testing, and forensic DNA profiling. In oncology, microsatellite instability, caused by mismatch repair deficiency, serves as a diagnostic and prognostic marker in several cancers, notably colorectal cancer and in Lynch syndrome screening.